Multiple Voltage Supply (MSV) chip fabrication is considered as a viable technique to address the power and thermal challenges of modern many-core systems. Efficiency of this technique has been demonstrated in application specific Network-on-Chips (NoCs) which have lots of cores and various operating voltages/frequencies. In this paper, a fourphase synthesis toolchain is proposed and evaluated for the design of multi-voltage application specific NoCs. The proposed synthesis toolchain performs i) core to router allocation, ii) voltage islanding to match voltages of cores connected to the same router, iii) hierarchical floorplanning to reduce the complexity of power delivery network, and iv) path allocation to connect routers based on the application requirements. The distinguishing feature of the proposed toolchain is that, for the first time, it performs the router allocation phase prior to voltage islanding. This offers more flexibility and more efficiency in the multi-voltage NoC synthesis. Experimental results on real world benchmarks show that the proposed toolchain provides 63% less energy consumption as well as more than double the design alternatives satisfying the benchmarks requirements compared to existing approaches.